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• 3D morphologies and time-dependent parameters of the hydrate shell are obtained. • Water is more mobile than gas in hydrates in the diffusion-controlled growth stage. • Protrusions growth on the outer surface of a hydrate shell is due to water permeation. • Effective diffusion coefficients of gas and water in hydrate are determined. Understanding the transport properties of water and guest molecules in dense hydrate structures is pivotal in controlling their formation and stability; this is nevertheless hindered by challenges in characterizing the time-varying diffusion and permeation process. This paper reports experimental results on the mass-transfer characteristics of water and guest molecules across hydrate shells during their formation from water droplets. The time-dependent 3D morphologies and parameters of hydrate shells were in-situ obtained via X-ray computed tomography to reveal the transport mechanism in hydrates. It was found that in the mass-transfer-limited stage, hydrate growth occurred primarily at the hydrate-gas interface, indicating a more mobile characteristic of water molecules in those hydrate shells than gas. The resulting outward permeation of water led to the growth of hydrate protrusions on the outer surface of the hydrate shell, suggesting a transition of the water transport schema through the hydrate shell from diffusion to permeation. Consequently, a diffusion-based shell growth model was developed to quantify the diffusivity of gas and water molecules in hydrates. Combining the measurements in the temperature range of 275.15–283.15 K, the effective diffusion coefficient of gas through the hydrates was estimated to be in the range of 1.34 × 10−14 − 1.90 × 10−13 m2/s, with that of interstitial water in the range of 2.87 × 10−12 − 3.83 × 10−11 m2/s. These results are of fundamental value in developing an improved understanding of the kinetics of hydrate formation from gas-water interfaces, which is essential in the optimization of hydrate-based techniques. [ABSTRACT FROM AUTHOR]